Browsing by Author "Katz, Barry"
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Item Acute Alcoholic Hepatitis: Natural History and Predictors of Mortality Using a Multicenter Prospective Study(Elsevier, 2017-04-28) Lourens, Spencer; Sunjaya, Dharma B.; Singal, Ashwani; Liangpunsakul, Suthat; Puri, Puneet; Sanyal, Arun; Ren, Xiaowei; Gores, Gregory J.; Radaeva, Svetlana; Chalasani, Naga; Crabb, David W.; Katz, Barry; Kamath, Patrick S.; Shah, Vijay H.; Biostatistics, School of Public HealthObjective: To examine the natural history of acute alcoholic hepatitis (AH) and identify predictors of mortality for AH using data from a prospective multicenter observational study. Participants and Methods: We analyzed data from 164 patients with AH and 131 heavy-drinking controls with no liver disease. Participants underwent clinical/laboratory assessment at baseline and 6 and 12 months after enrollment. Multivariable analyses were conducted to identify variables associated with mortality and examine the association between coffee drinking and risk of AH. Results: Thirty-six patients with AH died during follow-up, with estimated 30-day, 90-day, 180-day, and 1-year survival of 0.91 (95% CI, 0.87-0.96), 0.85 (95% CI, 0.80-0.91), 0.80 (95% CI, 0.74-0.87), and 0.75 (95% CI, 0.68-0.83), respectively. In the multivariable analysis, higher serum bilirubin level (hazard ratio [HR]=1.059; 95% CI, 1.022-1.089), lower hemoglobin level (HR=1.263; 95% CI, 1.012-1.575), and lower platelet count (HR=1.006; 95% CI, 1.001-1.012) were independently associated with mortality in AH. Compared with controls, fewer patients with AH regularly consumed coffee (20% vs 44%; P<.001), and this association between regular coffee drinking and lower risk of AH persisted after controlling for relevant covariates (odds ratio=0.26; 95% CI, 0.15-0.46). Time-dependent receiver operating characteristic curve analysis revealed that Model for End-Stage Liver Disease; Maddrey Discriminant Function; age, serum bilirubin, international normalized ratio, and serum creatinine; and Child-Pugh scores all provided similar discrimination performance at 30 days (area under the curve=0.73-0.77). Conclusion: Alcoholic hepatitis remains highly fatal, with 1-year mortality of 25%. Regular coffee consumption was associated with lower risk of AH in heavy drinkers.Item Acute Sport Concussion Assessment Optimization: A Prospective Assessment from the CARE Consortium(Springer, 2019) Broglio, Steven P.; Harezlak, Jaroslaw; Katz, Barry; Zhao, Shi; McAllister, Thomas; McCrea, Michael; Biostatistics, School of Public HealthBackground Numerous medical organizations recommend a multifaceted approach to the assessment of concussion occurring during sporting events. A number of tools are available to clinicians, with a wide breadth of sensitivity and specificity; however, little work has been done to evaluate the combined efficiency of these tools in concussed male and female athletes from a broad array of collegiate sports and with variable time from the pre-season baseline evaluation. Objective The aim of this study was to optimize the concussion assessment battery for application within the first 72 h of injury, and to identify the necessary baseline retesting frequency. Methods Between 2014 and 2017, a total of 1458 National Collegiate Athletic Association (NCAA) athletes sustaining 1640 diagnosed concussions completed a baseline assessment each year of the investigation and were evaluated up to three times within the first 72 h of injury using a standardized assessment protocol. Classification and regression tree analyses were implemented to identify the most efficient multifaceted assessment pathway to quantify concussion-related outcomes. Results were optimized for assessments occurring within 1 h post-injury, 1–24 h post-injury, and 24–72 h post-injury when using the raw post-injury assessment performance, difference scores from baseline evaluations occurring in the same year, and difference scores from baseline evaluations occurring the year prior. Results At each of the assessment time points, the analyses indicated that alone or in combination, a symptom evaluation, Balance Error Scoring System (BESS) scores collected on the firm surface, and Standardized Assessment of Concussion (SAC) total score offered the best overall performance when compared with pre-morbid performance captured in the same season. Optimized sensitivity of the multifaceted approach was 61% within 1 h of injury, 67% at the 1–24 h interval, and 55% at the 24–72 h interval when difference scores from the same-season baseline were available. Conclusions This investigation identified key concussion assessments in quantifying post-concussion performance among student athletes, that were maximized when same-season pre-morbid evaluations were available. Consistent with clinical recommendations, medical professionals should continue to focus on symptom reporting, postural control, and neurocognitive screening to support the clinical examination when making a concussion diagnosis.Item Alcohol abstinence ameliorates the dysregulated immune profiles in patients with alcoholic hepatitis: A prospective observational study(Wiley, 2017) Li, Wei; Amet, Tohti; Xing, Yanyan; Yang, Dennis; Liangpunsakul, Suthat; Puri, Puneet; Kamath, Patrick; Sanyal, Arun; Shah, Vijay; Katz, Barry; Radaeva, Svetlana; Crabb, David; Chalasani, Naga; Yu, Qigui; Department of Microbiology and Immunology, IU School of MedicineAlcoholic hepatitis (AH) develops in only a small proportion of heavy drinkers. To better understand the mechanisms underlying this disparity, we conducted a study to define the relationship between AH development and dysregulated immune responses that might be ameliorated by alcohol abstinence. Sixty-eight AH patients, 65 heavy drinking controls without liver disease (HDC), and 20 healthy controls were enrolled and followed up to 12 months. At baseline, HDC and healthy controls had no significant differences in their plasma levels of 38 inflammatory cytokines/chemokines measured using multiplex immunoassays. However, compared to HDC, AH patients had higher baseline levels of 11 cytokines/chemokines (tumor necrosis factor alpha, interleukin 6 [IL-6], IL-8, interferon gamma–induced protein 10, IL-4, IL-9, IL-10, fibroblast growth factor 2, IL-7, IL-15, and transforming growth factor alpha) but lower levels of the anti-inflammatory macrophage-derived chemokine. AH patients also had more activated yet dysfunctional immune cells as monocytes, T cells, and B cells expressed higher levels of cluster of differentiation 38 (CD38) and CD69 but low levels of human leukocyte antigen DR, CD80, and CD86 at baseline. In addition, CD4 T cells produced less interferon-gamma in response to T-cell stimulation. Up-regulated IL-6, IL-8, CD38, and CD69 and down-regulated macrophage-derived chemokine, human leukocyte antigen DR, CD86, and CD80 correlated positively and negatively, respectively, with disease severity. Longitudinal analysis indicated that levels of IL-6, IL-8, CD38, and CD69 were reduced, whereas levels of macrophage-derived chemokine, human leukocyte antigen DR, CD80, and CD86 were increased in abstinent AH patients. All of the cellular immune abnormalities were reversed by day 360 in abstinent AH patients; however, plasma levels of tumor necrosis factor alpha, IL-8, IL-10, fibroblast growth factor 2, and IL-7 remained higher. Conclusion: AH patients were in a highly immune-dysregulated state, whereas HDC showed little evidence of immune activation; alcohol abstinence reversed most, but not all, of the immunological abnormalities.Item Assessment of Blood Biomarker Profile After Acute Concussion During Combative Training Among US Military Cadets(JAMA, 2021-02) Giza, Christopher C.; McCrea, Michael; Huber, Daniel; Cameron, Kenneth L.; Houston, Megan N.; Jackson, Jonathan C.; McGinty, Gerald; Pasquina, Paul; Broglio, Steven P.; Brooks, Alison; DiFiori, John; Duma, Stefan; Harezlak, Jaroslaw; Goldman, Joshua; Guskiewicz, Kevin; McAllister, Thomas W.; McArthur, David; Meier, Timothy B.; Mihalik, Jason P.; Nelson, Lindsay D.; Rowson, Steven; Gill, Jessica; Foroud, Tatiana; Katz, Barry; Saykin, Andrew; Campbell, Darren E.; Svoboda, Steven; Psychiatry, School of MedicineImportance: Validation of protein biomarkers for concussion diagnosis and management in military combative training is important, as these injuries occur outside of traditional health care settings and are generally difficult to diagnose. Objective: To investigate acute blood protein levels in military cadets after combative training-associated concussions. Design, setting, and participants: This multicenter prospective case-control study was part of a larger cohort study conducted by the National Collegiate Athletic Association and the US Department of Defense Concussion Assessment Research and Education (CARE) Consortium from February 20, 2015, to May 31, 2018. The study was performed among cadets from 2 CARE Consortium Advanced Research Core sites: the US Military Academy at West Point and the US Air Force Academy. Cadets who incurred concussions during combative training (concussion group) were compared with cadets who participated in the same combative training exercises but did not incur concussions (contact-control group). Clinical measures and blood sample collection occurred at baseline, the acute postinjury point (<6 hours), the 24- to 48-hour postinjury point, the asymptomatic postinjury point (defined as the point at which the cadet reported being asymptomatic and began the return-to-activity protocol), and 7 days after return to activity. Biomarker levels and estimated mean differences in biomarker levels were natural log (ln) transformed to decrease the skewness of their distributions. Data were collected from August 1, 2016, to May 31, 2018, and analyses were conducted from March 1, 2019, to January 14, 2020. Exposure: Concussion incurred during combative training. Main outcomes and measures: Proteins examined included glial fibrillary acidic protein, ubiquitin C-terminal hydrolase-L1, neurofilament light chain, and tau. Quantification was conducted using a multiplex assay (Simoa; Quanterix Corp). Clinical measures included the Sport Concussion Assessment Tool-Third Edition symptom severity evaluation, the Standardized Assessment of Concussion, the Balance Error Scoring System, and the 18-item Brief Symptom Inventory. Results: Among 103 military service academy cadets, 67 cadets incurred concussions during combative training, and 36 matched cadets who engaged in the same training exercises did not incur concussions. The mean (SD) age of cadets in the concussion group was 18.6 (1.3) years, and 40 cadets (59.7%) were male. The mean (SD) age of matched cadets in the contact-control group was 19.5 (1.3) years, and 25 cadets (69.4%) were male. Compared with cadets in the contact-control group, those in the concussion group had significant increases in glial fibrillary acidic protein (mean difference in ln values, 0.34; 95% CI, 0.18-0.50; P < .001) and ubiquitin C-terminal hydrolase-L1 (mean difference in ln values, 0.97; 95% CI, 0.44-1.50; P < .001) levels at the acute postinjury point. The glial fibrillary acidic protein level remained high in the concussion group compared with the contact-control group at the 24- to 48-hour postinjury point (mean difference in ln values, 0.22; 95% CI, 0.06-0.38; P = .007) and the asymptomatic postinjury point (mean difference in ln values, 0.21; 95% CI, 0.05-0.36; P = .01). The area under the curve for all biomarkers combined, which was used to differentiate cadets in the concussion and contact-control groups, was 0.80 (95% CI, 0.68-0.93; P < .001) at the acute postinjury point. Conclusions and relevance: This study's findings indicate that blood biomarkers have potential for use as research tools to better understand the pathobiological changes associated with concussion and to assist with injury identification and recovery from combative training-associated concussions among military service academy cadets. These results extend the previous findings of studies of collegiate athletes with sport-associated concussions.Item The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis(Wiley, 2017) Puri, Puneet; Liangpunsakul, Suthat; Christensen, Jeffrey E.; Shah, Vijay H.; Kamath, Patrick S.; Gores, Gregory J.; Walker, Susan; Comerford, Megan; Katz, Barry; Borst, Andrew; Yu, Qigui; Kumar, Divya P.; Mirshahi, Faridoddin; Radaeva, Svetlana; Chalasani, Naga P.; Crabb, David W.; Sanyal, Arun J.; Medicine, School of MedicineIntestinal dysbiosis is implicated in alcoholic hepatitis (AH). However, changes in the circulating microbiome, its association with the presence and severity of AH and its functional relevance in AH is unknown. Qualitative and quantitative assessment of changes in the circulating microbiome were performed by sequencing bacterial DNA in subjects with moderate (n=18) or severe AH (n=19). These data were compared to heavy drinking controls (HDC) without obvious liver disease (n=19) and non-alcohol consuming controls (NAC, n=20). The data were related to endotoxin levels and markers of monocyte activation. Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis, inferred metagenomics and predictive functional analysis using PICRUSt were performed. There was a significant increase in 16S copies/ng DNA both in MAH (p<0.01) and SAH (p<0.001) subjects. Compared to NAC, the relative abundance of phylum Bacteroidetes was significantly decreased in HDC, MAH, and SAH (p<0.001). In contrast, all alcohol consuming groups had enrichment with Fusobacteria; this was greatest for HDC and decreased progressively in MAH and SAH. Subjects with SAH had significantly higher endotoxemia (p=0.01). Compared to alcohol consuming groups, predictive functional metagenomics indicated an enrichment of bacteria with genes related to methanogenesis and denitrification. Also, both HDC and SAH showed activation of type III secretion system which has been linked to gram negative bacterial virulence. Metagenomics in SAH vs NAC predicted increased isoprenoid synthesis via mevalonate and anthranilate degradation, known modulators of gram positive bacterial growth and biofilm production respectively. In conclusion, heavy alcohol consumption appears to be the primary driver of changes in the circulating microbiome associated with a shift in its inferred metabolic functions.Item classCleaner: A Quantitative Method for Validating Peptide Identification in LC-MS/MS Workflows(2020-05) Key, Melissa Chester; Boukai, Benzion; Ragg, Susanne; Katz, Barry; Mosley, AmberBecause label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) shotgun proteomics infers the peptide sequence of each measurement, there is inherent uncertainty in the identity of each peptide and its originating protein. Removing misidentified peptides can improve the accuracy and power of downstream analyses when differences between proteins are of primary interest. In this dissertation I present classCleaner, a novel algorithm designed to identify misidentified peptides from each protein using the available quantitative data. The algorithm is based on the idea that distances between peptides belonging to the same protein are stochastically smaller than those between peptides in different proteins. The method first determines a threshold based on the estimated distribution of these two groups of distances. This is used to create a decision rule for each peptide based on counting the number of within-protein distances smaller than the threshold. Using simulated data, I show that classCleaner always reduces the proportion of misidentified peptides, with better results for larger proteins (by number of constituent peptides), smaller inherent misidentification rates, and larger sample sizes. ClassCleaner is also applied to a LC-MS/MS proteomics data set and the Congressional Voting Records data set from the UCI machine learning repository. The later is used to demonstrate that the algorithm is not specific to proteomics.Item Detection of Rectal Chlamydia trachomatis in Heterosexual Men Who Report Cunnilingus(Wolters Kluwer, 2019-07-01) Batteiger, Teresa A.; Jordan, Stephen J.; Toh, Evelyn; Fortenberry, Lora; Williams, James A.; LaPradd, Michelle; Katz, Barry; Fortenberry, J. Dennis; Dodge, Brian; Arno, Janet; Batteiger, Byron E.; Nelson, David E.; Microbiology and Immunology, School of MedicineBackground. Rectal infection with Chlamydia trachomatis (CT) is frequent in women who deny receptive anal sex and is thought to arise from autoinoculation of the rectum from vaginal secretions. An alternate hypothesis is that oral sex inoculates and establishes gastrointestinal tract infection. Distinguishing these hypotheses is difficult in women. In men, autoinoculation is unlikely and heterosexual men frequently perform oral sex, but rarely participate in receptive anal exposure behaviors. Methods. We enrolled high-risk men with and without nongonococcal urethritis (NGU) who presented to a sexually transmitted infection clinic in Indianapolis, Indiana. Urine and rectal swabs were collected and tested for urogenital and rectal CT, Neisseria gonorrhoeae (NG), and Mycoplasma genitalium (MG). Men completed surveys concerning symptoms, sexual orientation, and detailed recent and lifetime oral and anal sexual behaviors. Results. Rectal CT was detected in 2/84 (2.4%) heterosexual men who reported cunnilingus, but no lifetime receptive anal behaviors. All of the men who denied receptive anal behaviors were negative for rectal NG and MG. In homosexual and bisexual men, rectal CT prevalence was high (9.7%) and rectal NG (4.8%) and MG (4.8%) were also detected. Conclusions. We detected rectal CT infections in heterosexual men who reported cunnilingus but denied receptive anal behaviors. Oral sex may be a risk factor for rectal CT infection via oral inoculation of the gastrointestinal tract. Summary. We observed a low incidence of rectal C. trachomatis infection in heterosexual men.Item Effects of Age, Sex, Body Weight, and Quantity of Alcohol Consumption on Occurrence and Severity of Alcoholic Hepatitis(Elsevier, 2016-12) Liangpunsakul, Suthat; Puri, Puneet; Shah, Vijay; Kamath, Patrick; Sanyal, Arun; Urban, Thomas; Ren, Xiaowei; Katz, Barry; Radaeva, Svetlana; Chalasani, Naga; Crabb, David W.; Medicine, School of MedicineBackground & Aims Only a minority of heavy drinking individuals develop alcoholic hepatitis (AH), for unclear reasons. We analyzed data from the Translational Research and Evolving Alcoholic Hepatitis Treatment cohort: subjects who drink heavily with normal results from liver tests (controls) and patients with AH. We examined risk factors for the development of AH including body mass index (BMI), drinking pattern and quantity, and sex. Methods We compared data from 145 patients with AH cases and 124 controls, based on BMI when they joined the cohort; groups were matched for sex and race. Drinking patterns were assessed using the time line follow back method, the Alcohol Use Disorders Identification Test, and National Institute of Alcohol Abuse and Alcoholism 6-question survey. We performed univariable and multivariable analyses we to assess effects of these factors and their interaction in increasing the risk for AH. We also explored the association between PNPLA3 variants and AH. Results Cases with AH were older (47 vs 44 years; P=.03). For nearly all measures of quantity of alcohol consumed or frequency of binge drinking, controls drank more heavily than cases with AH. We did not find an association between BMI, sex, drinking patterns, and the presence of AH. Age and BMI were independent predictors for severity of AH. When we analyzed cases and controls of European ancestry, the PNPLA3 single nucleotide polymorphism rs738409 was associated with risk for AH (odds ratio, 1.89; P=.007). Conclusion Compared with heavy drinkers without liver disease, subjects with AH consumed lower levels of alcohol and had less binge drinking, suggesting an increased sensitivity to the toxic effects of alcohol. The risk for AH may be associated with the PNPLA3 rs738409 polymorphism.Item Joint modeling of bivariate time to event data with semi-competing risk(2016-09-08) Liao, Ran; Gao, Sujuan; Katz, Barry; Zhang, Ying; Li, Shanshan; Zhang, JianjunSurvival analysis often encounters the situations of correlated multiple events including the same type of event observed from siblings or multiple events experienced by the same individual. In this dissertation, we focus on the joint modeling of bivariate time to event data with the estimation of the association parameters and also in the situation of a semi-competing risk. This dissertation contains three related topics on bivariate time to event mod els. The first topic is on estimating the cross ratio which is an association parameter between bivariate survival functions. One advantage of using cross-ratio as a depen dence measure is that it has an attractive hazard ratio interpretation by comparing two groups of interest. We compare the parametric, a two-stage semiparametric and a nonparametric approaches in simulation studies to evaluate the estimation perfor mance among the three estimation approaches. The second part is on semiparametric models of univariate time to event with a semi-competing risk. The third part is on semiparametric models of bivariate time to event with semi-competing risks. A frailty-based model framework was used to accommodate potential correlations among the multiple event times. We propose two estimation approaches. The first approach is a two stage semiparametric method where cumulative baseline hazards were estimated by nonparametric methods first and used in the likelihood function. The second approach is a penalized partial likelihood approach. Simulation studies were conducted to compare the estimation accuracy between the proposed approaches. Data from an elderly cohort were used to examine factors associated with times to multiple diseases and considering death as a semi-competing risk.Item A multivariate finite mixture latent trajectory model with application to dementia studies(Taylor & Francis, 2016) Lai, Dongbing; Xu, Huiping; Katz, Barry; Koller, Daniel; Foroud, Tatiana; Gao, Sujuan; Department of Biostatistics, Richard M. Fairbanks School of Public HealthDementia patients exhibit considerable heterogeneity in individual trajectories of cognitive decline, with some patients showing rapid decline following diagnoses while others exhibiting slower decline or remaining stable for several years. Dementia studies often collect longitudinal measures of multiple neuropsychological tests aimed to measure patients’ decline across a number of cognitive domains. We propose a multivariate finite mixture latent trajectory model to identify distinct longitudinal patterns of cognitive decline simultaneously in multiple cognitive domains, each of which is measured by multiple neuropsychological tests. EM algorithm is used for parameter estimation and posterior probabilities are used to predict latent class membership. We present results of a simulation study demonstrating adequate performance of our proposed approach and apply our model to the Uniform Data Set from the National Alzheimer's Coordinating Center to identify cognitive decline patterns among dementia patients.